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Coexpression cluster:C490: Difference between revisions

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|full_id=C490_Hair_Fibroblast_Synoviocyte_Olfactory_Preadipocyte_Endothelial_Osteoblast
|full_id=C490_Hair_Fibroblast_Synoviocyte_Olfactory_Preadipocyte_Endothelial_Osteoblast
|id=C490
|id=C490
|ontology_enrichment_celltype=CL:0000055!5.72e-34!180;CL:0002371!1.47e-29!591;CL:0000144!7.23e-26!625;CL:0000048!1.39e-21!430;CL:0000723!5.02e-20!436;CL:0000057!6.26e-19!75;CL:0000034!1.31e-18!444;CL:0000222!1.24e-17!119;CL:0000548!1.33e-15!679;CL:0000004!1.33e-15!679;CL:0000255!1.33e-15!679;CL:0000012!2.31e-15!682;CL:0000680!9.29e-14!57;CL:0000056!9.29e-14!57;CL:0000355!9.29e-14!57;CL:0000183!1.43e-13!59;CL:0000187!3.38e-13!54;CL:0000393!3.51e-12!60;CL:0000211!3.51e-12!60;CL:0000192!7.30e-11!42;CL:0000514!7.30e-11!42;CL:0002320!1.02e-10!365;CL:0000003!1.82e-10!722;CL:0000219!1.96e-09!390;CL:0000359!2.10e-09!32;CL:0000134!3.65e-09!358;CL:0002620!3.91e-09!23
|ontology_enrichment_celltype=CL:0002371!8.10e-29!588;CL:0000048!3.24e-21!427;CL:0000723!9.81e-20!433;CL:0000057!6.00e-19!76;CL:0000034!4.17e-18!441;CL:0000222!1.16e-17!121;CL:0000548!4.11e-15!679;CL:0000255!4.11e-15!679;CL:0000055!1.11e-13!106;CL:0000680!2.89e-13!58;CL:0000056!2.89e-13!58;CL:0000355!2.89e-13!58;CL:0000183!7.64e-13!59;CL:0000187!1.00e-12!55;CL:0000393!1.17e-11!61;CL:0000211!1.17e-11!61;CL:0000192!9.28e-11!43;CL:0000514!9.28e-11!43;CL:0002320!1.32e-10!361;CL:0000003!4.81e-10!722;CL:0000219!2.76e-09!386;CL:0000359!3.04e-09!32;CL:0000134!4.34e-09!354;CL:0002620!7.27e-09!23;CL:0000473!1.95e-07!48;CL:0000234!1.95e-07!48;CL:0000325!4.09e-07!87;CL:0002009!5.33e-07!61
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003081!4.31e-20!216;UBERON:0002204!5.87e-20!167;UBERON:0000914!7.51e-18!83;UBERON:0002329!7.51e-18!83;UBERON:0003077!7.51e-18!83;UBERON:0003059!7.51e-18!83;UBERON:0007282!7.51e-18!83;UBERON:0009618!7.51e-18!83;UBERON:0007285!7.51e-18!83;UBERON:0002049!1.13e-17!79;UBERON:0007798!1.13e-17!79;UBERON:0004535!1.15e-17!110;UBERON:0001009!1.66e-16!113;UBERON:0004290!2.44e-16!70;UBERON:0004872!2.07e-15!84;UBERON:0000055!3.22e-15!69;UBERON:0001981!2.56e-14!60;UBERON:0007500!2.56e-14!60;UBERON:0004537!2.56e-14!60;UBERON:0006965!2.56e-14!60;UBERON:0000486!6.12e-14!82;UBERON:0001637!1.65e-13!42;UBERON:0003509!1.65e-13!42;UBERON:0004572!1.65e-13!42;UBERON:0000926!3.66e-13!448;UBERON:0004120!3.66e-13!448;UBERON:0006603!3.66e-13!448;UBERON:0001134!1.58e-12!61;UBERON:0002036!1.58e-12!61;UBERON:0003082!1.58e-12!61;UBERON:0002385!7.77e-12!63;UBERON:0001015!7.77e-12!63;UBERON:0000383!7.77e-12!63;UBERON:0002384!8.06e-11!375;UBERON:0004573!1.65e-10!33;UBERON:0004571!1.65e-10!33;UBERON:0003914!2.87e-08!118;UBERON:0005256!9.33e-08!143;UBERON:0004765!9.54e-08!101;UBERON:0001434!9.54e-08!101;UBERON:0002199!1.60e-07!45;UBERON:0002416!1.60e-07!45;UBERON:0000468!1.99e-07!659;UBERON:0000947!3.52e-07!21;UBERON:0010191!3.52e-07!21;UBERON:0001013!4.48e-07!14
|ontology_enrichment_uberon=UBERON:0000926!4.91e-27!315;UBERON:0004120!4.91e-27!315;UBERON:0006603!4.91e-27!315;UBERON:0002204!2.40e-21!167;UBERON:0003081!1.79e-19!203;UBERON:0004535!1.67e-17!109;UBERON:0002049!2.65e-17!78;UBERON:0007798!2.65e-17!78;UBERON:0001009!2.46e-16!112;UBERON:0007503!2.91e-16!78;UBERON:0007524!5.62e-16!73;UBERON:0002329!7.07e-16!71;UBERON:0003059!7.07e-16!71;UBERON:0007282!7.07e-16!71;UBERON:0004290!7.07e-16!71;UBERON:0009618!7.07e-16!71;UBERON:0003077!1.97e-15!72;UBERON:0007285!1.97e-15!72;UBERON:0004872!6.07e-15!83;UBERON:0000055!7.81e-15!68;UBERON:0007500!7.14e-14!59;UBERON:0001981!7.14e-14!59;UBERON:0004537!7.14e-14!59;UBERON:0006965!7.14e-14!59;UBERON:0000486!2.04e-13!83;UBERON:0001637!3.32e-13!42;UBERON:0003509!3.32e-13!42;UBERON:0004572!3.32e-13!42;UBERON:0001134!5.89e-12!62;UBERON:0002036!5.89e-12!62;UBERON:0003082!5.89e-12!62;UBERON:0002385!2.80e-11!64;UBERON:0001015!2.80e-11!64;UBERON:0000383!2.80e-11!64;UBERON:0002384!1.12e-10!371;UBERON:0004573!3.50e-10!33;UBERON:0004571!3.50e-10!33;UBERON:0001434!3.93e-09!100;UBERON:0000490!5.66e-09!148;UBERON:0003914!1.34e-08!117;UBERON:0002199!3.86e-08!46;UBERON:0002416!3.86e-08!46;UBERON:0000468!4.32e-08!656;UBERON:0000480!1.00e-07!625;UBERON:0000467!1.24e-07!624;UBERON:0004765!2.15e-07!90;UBERON:0003104!3.15e-07!160;UBERON:0009142!3.15e-07!160;UBERON:0001013!4.63e-07!14;UBERON:0000947!6.76e-07!21;UBERON:0010191!6.76e-07!21
|tf_chipseq_enrich=CTCF#10664;15:4.2317813471645:2.07084251553897e-08:1.47427894669649e-06!POLR2A#5430;17:1.92140547376248:0.000122324795069828:0.00164866166889893!SETDB1#9869;4:8.48842656379168:0.00108665641766437:0.0075983737014227!SP1#6667;9:2.69923328438253:0.00265747422100205:0.0146662412897502!ZBTB33#10009;5:8.33282237631083:0.000251606689417626:0.00271014346494301
|tf_chipseq_enrich=CTCF#10664;15:4.2317813471645:2.07084251553897e-08:1.47427894669649e-06!POLR2A#5430;17:1.92140547376248:0.000122324795069828:0.00164866166889893!SETDB1#9869;4:8.48842656379168:0.00108665641766437:0.0075983737014227!SP1#6667;9:2.69923328438253:0.00265747422100205:0.0146662412897502!ZBTB33#10009;5:8.33282237631083:0.000251606689417626:0.00271014346494301
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Revision as of 16:19, 19 October 2012


Full id: C490_Hair_Fibroblast_Synoviocyte_Olfactory_Preadipocyte_Endothelial_Osteoblast



Phase1 CAGE Peaks

Hg19::chr10:17271510..17271558,-p2@uc001iot.1
Hg19::chr10:17271561..17271615,-p4@uc001iot.1
Hg19::chr10:17271691..17271750,-p3@uc001iot.1
Hg19::chr10:17271757..17271791,-p6@uc001iot.1
Hg19::chr10:17271821..17271858,-p7@uc001iot.1
Hg19::chr10:17271866..17271897,-p5@uc001iot.1
Hg19::chr10:17272666..17272724,-p@chr10:17272666..17272724
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Hg19::chr10:17275793..17275820,-p@chr10:17275793..17275820
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Hg19::chr10:17275853..17275926,-p@chr10:17275853..17275926
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Hg19::chr10:17276719..17276781,-p1@ENST00000456355
Hg19::chr10:17276801..17276827,-p5@ENST00000456355
Hg19::chr10:17277201..17277219,-p4@ENST00000456355
Hg19::chr10:17277221..17277254,-p3@ENST00000456355
Hg19::chr10:17277255..17277323,-p2@ENST00000456355
Hg19::chr10:17277365..17277388,-p@chr10:17277365..17277388
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Hg19::chr10:17278325..17278353,-p@chr10:17278325..17278353
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Hg19::chr10:17278354..17278389,-p@chr10:17278354..17278389
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Hg19::chr10:17279298..17279334,-p1@CU674071
Hg19::chr10:17279393..17279433,-p2@CU674071


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
somatic cell8.10e-29588
multi fate stem cell3.24e-21427
somatic stem cell9.81e-20433
fibroblast6.00e-1976
stem cell4.17e-18441
mesodermal cell1.16e-17121
animal cell4.11e-15679
eukaryotic cell4.11e-15679
non-terminally differentiated cell1.11e-13106
muscle precursor cell2.89e-1358
myoblast2.89e-1358
multi-potent skeletal muscle stem cell2.89e-1358
contractile cell7.64e-1359
muscle cell1.00e-1255
electrically responsive cell1.17e-1161
electrically active cell1.17e-1161
smooth muscle cell9.28e-1143
smooth muscle myoblast9.28e-1143
connective tissue cell1.32e-10361
native cell4.81e-10722
motile cell2.76e-09386
vascular associated smooth muscle cell3.04e-0932
mesenchymal cell4.34e-09354
skin fibroblast7.27e-0923
defensive cell1.95e-0748
phagocyte1.95e-0748
stuff accumulating cell4.09e-0787
macrophage dendritic cell progenitor5.33e-0761
Uber Anatomy
Ontology termp-valuen
mesoderm4.91e-27315
mesoderm-derived structure4.91e-27315
presumptive mesoderm4.91e-27315
musculoskeletal system2.40e-21167
lateral plate mesoderm1.79e-19203
cardiovascular system1.67e-17109
vasculature2.65e-1778
vascular system2.65e-1778
circulatory system2.46e-16112
epithelial vesicle2.91e-1678
dense mesenchyme tissue5.62e-1673
somite7.07e-1671
presomitic mesoderm7.07e-1671
presumptive segmental plate7.07e-1671
dermomyotome7.07e-1671
trunk paraxial mesoderm7.07e-1671
paraxial mesoderm1.97e-1572
presumptive paraxial mesoderm1.97e-1572
splanchnic layer of lateral plate mesoderm6.07e-1583
vessel7.81e-1568
epithelial tube open at both ends7.14e-1459
blood vessel7.14e-1459
blood vasculature7.14e-1459
vascular cord7.14e-1459
multilaminar epithelium2.04e-1383
artery3.32e-1342
arterial blood vessel3.32e-1342
arterial system3.32e-1342
skeletal muscle tissue5.89e-1262
striated muscle tissue5.89e-1262
myotome5.89e-1262
muscle tissue2.80e-1164
musculature2.80e-1164
musculature of body2.80e-1164
connective tissue1.12e-10371
systemic artery3.50e-1033
systemic arterial system3.50e-1033
skeletal system3.93e-09100
unilaminar epithelium5.66e-09148
epithelial tube1.34e-08117
integument3.86e-0846
integumental system3.86e-0846
multi-cellular organism4.32e-08656
anatomical group1.00e-07625
anatomical system1.24e-07624
skeletal element2.15e-0790
mesenchyme3.15e-07160
entire embryonic mesenchyme3.15e-07160
adipose tissue4.63e-0714
aorta6.76e-0721
aortic system6.76e-0721


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

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ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#10664154.23178134716452.07084251553897e-081.47427894669649e-06
POLR2A#5430171.921405473762480.0001223247950698280.00164866166889893
SETDB1#986948.488426563791680.001086656417664370.0075983737014227
SP1#666792.699233284382530.002657474221002050.0146662412897502
ZBTB33#1000958.332822376310830.0002516066894176260.00271014346494301



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.